• Rytas J. Vilgalys

  • Professor and Assistant Professor of Molecular Genetics and Microbiology
  • Duke Herbarium
  • Room 137, Biological Sciences Building, 130 Science Drive, Durham, NC 27708
  • Campus Box 90338
  • Phone: (919) 660-7361
  • Fax: (919) 660-7293
  • Homepage
  • Curriculum Vitae
  • Specialties

    • Fungi
  • Teaching

    • BIOLOGY 557L.01
      • MICROBIAL ECOL/EVOL
      • French Sci 1244
      • TuTh 08:30 AM-11:30 AM
  • Education

      • Ph.D.,
      • Virginia Polytech Institute and State University,
      • 1985
      • MS Botany,
      • Virginia Tech,
      • 1982
      • M.S.,
      • Virginia Polytech Institute and State University,
      • 1981
      • BA Botany,
      • State University of New York College at Geneseo,
      • 1978
      • B.A.,
      • State University of New York at Geneseo,
      • 1978
  • Awards, Honors and Distinctions

      • see cv,
      • December, 2007
      • New York State Regents Scholarship,
      • 1975-1978
      • MSA Fellows,
      • Mycological Society of America,
      • January 2002
      • AAAS Fellow,
      • 0 2002
      • Mid-Career Fellowship,
      • Mycological Society of America,
      • 0 2002
      • Alexopoulos Prize,
      • Mycological Society of America,
      • January 1995
      • Alexopolous Award,
      • Mycological Society of America,
      • 0 1995
      • Outstanding dissertation award,
      • College of Arts and Sciences, Virginia Tech,
      • 0 1986
      • Gertrude S. Burlingham Fellowship,
      • New York Botanical Garden,
      • 0 1983
  • Selected Publications

      • MS Benítez, MH Hersh, R Vilgalys and JS Clark.
      • (December, 2013).
      • Pathogen regulation of plant diversity via effective specialization..
      • Trends Ecol Evol
      • ,
      • 28
      • (12)
      • ,
      • 705-711.
      • [web]
      Publication Description

      The Janzen-Connell (JC) hypothesis, one of the most influential hypotheses explaining forest diversity, is inconsistent with evidence that tree species share the same natural enemies. Through the discussion of seedling diseases from a pathogen-centered perspective, we expand the JC hypothesis to tie in host-pathogen-environment interactions at three levels: local adaptation, host specificity of the combined effect of multiple infections, and environmental modulation of disease. We present evidence from plant pathology, disease ecology, and host-parasite evolution relevant to (but not commonly associated with) forest species diversity maintenance. This expanded view of the JC hypothesis suggests ways to direct new experiments to integrate research on pathogen local adaptation, co-infection, and environmental effects on infection by using high-throughput molecular techniques and statistical models.

      • AP Gryganskyi, RA Humber, JE Stajich, B Mullens, IM Anishchenko and R Vilgalys.
      • (2013).
      • Sequential Utilization of Hosts from Different Fly Families by Genetically Distinct, Sympatric Populations within the Entomophthora muscae Species Complex.
      • PLoS ONE
      • ,
      • 8
      • (8)
      • ,
      • e71168.
      • [web]
      Publication Description

      The fungus Entomophthora muscae (Entomophthoromycota, Entomophthorales, Entomophthoraceae) is a widespread insect pathogen responsible for fatal epizootic events in many dipteran fly hosts. During epizootics in 2011 and 2012 in Durham, North Carolina, we observed a transition of fungal infections from one host, the plant-feeding fly Delia radicum, to a second host, the predatory fly Coenosia tigrina. Infections first appeared on Delia in the middle of March, but by the end of May, Coenosia comprised 100% of infected hosts. Multilocus sequence typing revealed that E. muscae in Durham comprises two distinct subpopulations (clades) with several haplotypes in each. Fungi from either clade are able to infect both fly species, but vary in their infection phenologies and host-specificities. Individuals of the more phylogenetically diverse clade I predominated during the beginning of the spring epizootic, infecting mostly phytophagous Delia flies. Clade II dominated in late April and May and affected mostly predatory Coenosia flies. Analysis of population structure revealed two subpopulations within E. muscae with limited gene exchange. This study provides the first evidence of recombination and population structure within the E. muscae species complex, and illustrates the complexity of insect-fungus relationships that should be considered for development of biological control methods.

      • G Bonito, ME Smith, M Nowak, RA Healy, G Guevara, E Cázares, A Kinoshita, ER Nouhra, LS Domínguez, L Tedersoo, C Murat, Y Wang, BA Moreno, DH Pfister, K Nara, A Zambonelli, JM Trappe and R Vilgalys.
      • (2013).
      • Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage..
      • PLoS One
      • ,
      • 8
      • (1)
      • ,
      • e52765.
      • [web]
      Publication Description

      Truffles have evolved from epigeous (aboveground) ancestors in nearly every major lineage of fleshy fungi. Because accelerated rates of morphological evolution accompany the transition to the truffle form, closely related epigeous ancestors remain unknown for most truffle lineages. This is the case for the quintessential truffle genus Tuber, which includes species with socio-economic importance and esteemed culinary attributes. Ecologically, Tuber spp. form obligate mycorrhizal symbioses with diverse species of plant hosts including pines, oaks, poplars, orchids, and commercially important trees such as hazelnut and pecan. Unfortunately, limited geographic sampling and inconclusive phylogenetic relationships have obscured our understanding of their origin, biogeography, and diversification. To address this problem, we present a global sampling of Tuberaceae based on DNA sequence data from four loci for phylogenetic inference and molecular dating. Our well-resolved Tuberaceae phylogeny shows high levels of regional and continental endemism. We also identify a previously unknown epigeous member of the Tuberaceae--the South American cup-fungus Nothojafnea thaxteri (E.K. Cash) Gamundí. Phylogenetic resolution was further improved through the inclusion of a previously unrecognized Southern hemisphere sister group of the Tuberaceae. This morphologically diverse assemblage of species includes truffle (e.g. Gymnohydnotrya spp.) and non-truffle forms that are endemic to Australia and South America. Southern hemisphere taxa appear to have diverged more recently than the Northern hemisphere lineages. Our analysis of the Tuberaceae suggests that Tuber evolved from an epigeous ancestor. Molecular dating estimates Tuberaceae divergence in the late Jurassic (~156 million years ago), with subsequent radiations in the Cretaceous and Paleogene. Intra-continental diversification, limited long-distance dispersal, and ecological adaptations help to explain patterns of truffle evolution and biodiversity.

      • Smith, M E and Henkel, T W and Uehling, J K and Fremier, A K and Clarke, H D and Vilgalys, R.
      • (2013).
      • The Ectomycorrhizal Fungal Community in a Neotropical Forest Dominated by the Endemic Dipterocarp Pakaraimaea dipterocarpacea.
      • PLoS ONE
      • ,
      • 8
      • (1)
      • ,
      • e55160.
      • CF Weber, R Vilgalys and CR Kuske.
      • (2013).
      • Changes in fungal community composition in response to elevated atmospheric CO2 and nitrogen fertilization varies with soil horizon.
      • Frontiers in Microbiology
      • ,
      • 4
      • (APR)
      • ,
      • 1--14.
      • [web]
      Publication Description

      Increasing levels of atmospheric carbon dioxide (CO2) and rates of nitrogen (N)-deposition to forest ecosystems are predicted to alter the structure and function of soil fungal communities, but the spatially heterogeneous distribution of soil fungi has hampered investigations aimed at understanding such impacts. We hypothesized that soil physical and chemical properties and fungal community composition would be differentially impacted by elevated atmospheric CO2 (eCO2) and N-fertilization in spatially separated field samples, in the forest floor, 0-2, 2-5, and 5-10 cm depth intervals in a loblolly pine Free-Air Carbon Dioxide Enrichment (FACE) experiment. In all soils, quantitative PCR-based estimates of fungal biomass were highest in the forest floor. Fungal richness, based on pyrosequencing of the fungal ribosomal large subunit gene, increased in response to N-fertilization in 0-2 cm and forest floor intervals. Composition shifted in forest floor, 0-2 and 2-5 cm intervals in response to N-fertilization, but the shift was most distinct in the 0-2 cm interval, in which the largest number of statistically significant changes in soil chemical parameters (i.e., phosphorus, organic matter, calcium, pH) was also observed. In the 0-2 cm interval, increased recovery of sequences from the Thelephoraceae, Tricholomataceae, Hypocreaceae, Clavicipitaceae, and Herpotrichiellaceae families and decreased recovery of sequences from the Amanitaceae correlated with N-fertilization. In this same depth interval, Amanitaceae, Tricholomataceae, and Herpotriciellaceae sequences were recovered less frequently from soils exposed to eCO2 relative to ambient conditions. These results demonstrated that vertical stratification should be taken into consideration in future efforts to elucidate environmental impacts on fungal communities and their feedbacks on ecosystem processes. © 2013 Weber, Vilgalys and Kuske.

      • M Shakya, N Gottel, H Castro, ZK Yang, L Gunter, J Labbé, W Muchero, G Bonito, R Vilgalys, G Tuskan and E al.
      • (2013).
      • A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees.
      • PLoS ONE
      • ,
      • 8
      • (10)
      • ,
      • e76382.
      • [web]
      Publication Description

      Bacterial and fungal communities associated with plant roots are central to the host health, survival and growth. However, a robust understanding of the root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to its associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall host genotypic distances did not have a significant effect on corresponding communities that could be separated from other measured effects. © 2013 Shakya et al.

      • MH Hersh, R Vilgalys and JS Clark.
      • (2012).
      • Evaluating the impacts of multiple generalist fungal pathogens on temperate tree seedling survival..
      • Ecology
      • ,
      • 93
      • (3)
      • ,
      • 511-520.
      • [web]
      Publication Description

      Host-specific mortality driven by natural enemies is a widely discussed mechanism for explaining plant diversity. In principle, populations of plant species can be regulated by distinct host-specific natural enemies that have weak or nonexistent effects on heterospecific competitors, preventing any single species from becoming dominant and thus promoting diversity. Two of the first steps in exploring the role of natural enemies in diversity regulation are to (1) identify potential enemies and (2) evaluate their levels of host specificity by determining if interactions between any one host and its enemy have equivalent survival impacts on co-occurring host species. We developed a bioinformatics framework to evaluate impacts of potential pathogens on seedling survival, for both single and multiple infections. Importantly, we consider scenarios not only if there are specialist pathogens for each plant, but also when generalist pathogens have differential effects on multiple host species, and when co-infection has species-specific effects. We then applied this analytical framework to a field experiment using molecular techniques to detect potential fungal pathogens on co-occurring tree seedling hosts. Combinatorial complexity created by 160 plant-fungus interactions was reduced to eight combinations that affect seedling survival. Potential fungal pathogens had broad host ranges, but seedling species were each regulated by different combinations of fungi or by generalist fungi that had differential effects on multiple plant species. Soil moisture can have the potential to shift the nature of the interactions in some plant-fungal combinations from neutral to detrimental. Reassessing the assumption of single-enemy-single-host interactions broadens the mechanisms through which natural enemies can influence plant diversity.

      • J Dunbar, SA Eichorst, LV Gallegos-Graves, S Silva, G Xie, NW Hengartner, RD Evans, BA Hungate, RB Jackson, JP Megonigal, CW Schadt, R Vilgalys, DR Zak and CR Kuske.
      • (2012).
      • Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide.
      • Environmental Microbiology
      • ,
      • 14
      • (5)
      • ,
      • 1145-1158.
      • [web]
      Publication Description

      Six terrestrial ecosystems in the USA were exposed to elevated atmospheric CO2 in single or multifactorial experiments for more than a decade to assess potential impacts. We retrospectively assessed soil bacterial community responses in all six-field experiments and found ecosystem-specific and common patterns of soil bacterial community response to elevated CO2. Soil bacterial composition differed greatly across the six ecosystems. No common effect of elevated atmospheric CO2 on bacterial biomass, richness and community composition across all of the ecosystems was identified, although significant responses were detected in individual ecosystems. The most striking common trend across the sites was a decrease of up to 3.5-fold in the relative abundance of Acidobacteria Group 1 bacteria in soils exposed to elevated CO2 or other climate factors. The Acidobacteria Group 1 response observed in exploratory 16S rRNA gene clone library surveys was validated in one ecosystem by 100-fold deeper sequencing and semi-quantitative PCR assays. Collectively, the 16S rRNA gene sequencing approach revealed influences of elevated CO2 on multiple ecosystems. Although few common trends across the ecosystems were detected in the small surveys, the trends may be harbingers of more substantive changes in less abundant, more sensitive taxa that can only be detected by deeper surveys. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

      • CF Weber, DR Zak, BA Hungate, RB Jackson, R Vilgalys, RD Evans, CW Schadt, JP Megonigal and CR Kuske.
      • (2011).
      • Responses of soil cellulolytic fungal communities to elevated atmospheric CO 2 are complex and variable across five ecosystems.
      • Environmental Microbiology
      • ,
      • 13
      • (10)
      • ,
      • 2778-2793.
      • [web]
      Publication Description

      Elevated atmospheric CO 2 generally increases plant productivity and subsequently increases the availability of cellulose in soil to microbial decomposers. As key cellulose degraders, soil fungi are likely to be one of the most impacted and responsive microbial groups to elevated atmospheric CO 2. To investigate the impacts of ecosystem type and elevated atmospheric CO 2 on cellulolytic fungal communities, we sequenced 10677 cbhI gene fragments encoding the catalytic subunit of cellobiohydrolase I, across five distinct terrestrial ecosystem experiments after a decade of exposure to elevated CO 2. The cbhI composition of each ecosystem was distinct, as supported by weighted Unifrac analyses (all P-values;<0.001), with few operational taxonomic units (OTUs) being shared across ecosystems. Using a 114-member cbhI sequence database compiled from known fungi, less than 1% of the environmental sequences could be classified at the family level indicating that cellulolytic fungi in situ are likely dominated by novel fungi or known fungi that are not yet recognized as cellulose degraders. Shifts in fungal cbhI composition and richness that were correlated with elevated CO 2 exposure varied across the ecosystems. In aspen plantation and desert creosote bush soils, cbhI gene richness was significantly higher after exposure to elevated CO 2 (550μmol mol -1) than under ambient CO 2 (360μmol mol -1 CO 2). In contrast, while the richness was not altered, the relative abundance of dominant OTUs in desert soil crusts was significantly shifted. This suggests that responses are complex, vary across different ecosystems and, in at least one case, are OTU-specific. Collectively, our results document the complexity of cellulolytic fungal communities in multiple terrestrial ecosystems and the variability of their responses to long-term exposure to elevated atmospheric CO 2. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

      • NR Gottel, HF Castro, M Kerley, Z Yang, DA Pelletier, M Podar, T Karpinets, E Uberbacher, GA Tuskan, R Vilgalys, MJ Doktycz and CW Schadt.
      • (2011).
      • Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types.
      • Applied and Environmental Microbiology
      • ,
      • 77
      • (17)
      • ,
      • 5934-5944.
      • [web]
      Publication Description

      The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis, regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere. © 2011, American Society for Microbiology.

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  • Postdoctoral Students

    • Gregory Bonito
      • 2009-20013
    • Sunny Liou
      • 2012-present
    • Soledad Benitez-Ponce
      • 2011-present
      • Soledad is working with Jim Clark and our lab on ecology of forest pathogens.
    • Brantlee Richter
      • 2010-2011
      • Brantlee worked with myself and Jim Clark on forest seedling pathology. Last February, she took a position as lecturer in the Dept. of Plant Pathology, Univ. of Florida. Good luck Brantlee!
    • Matthew Smith
      • 2009-2011
      • Matt recently landed a tenure track position as mycologist at the Univ. of Florida. Congratulations, Dr. Smith. This is also the son of a bitch who named a new lichen species after me!.
    • Teresa Porter
      • 2008 - 2010
      • Teri is the current postdoc on our NSF Tree of Life project. Her specialty areas include current approaches to study of fungal biodiversity, including molecular phylogenetics, and environmental genomics.
    • Andrii Grygansky
      • 2008-present
      • Andrii, a visiting scientist from the Ukraine, is investigating the phylogeny and mating biology of several diverse basal fungal lineages once known as Zygomycetes, including the human pathogen Rhizopus, as well as insect-pathogens belonging to the family Entomopthorales. Andrii is also contributing data to our NSF Fungal Tree of Life Project.
    • Timothy James
      • 2003 - 2006
      • current: Assistant Professor, Univ. Michigan
    • Annette Golonka
      • 2002 - 2006
      • current: Asst. Professor, Univ. So. Carolina at Lancaster
    • Valerie Hofstetter
      • 2002 - 2006
    • Ana Litvintseva
      • 2001 - 2006
      • Current: assistant research professor in the Dept. of Molecular Genetics and Microbiology, Duke University Medical Center
    • Austin Ganley
      • 2000 - 2002
      • current: Research Scientist, National Institute for Basic Biology, Aichi, Japan
    • Robert Marra
      • 2000 - 2003
      • current position: Research Scientist, The Connecticut Agricultural Experiment Station, New Haven, CT
    • Ursula Peintner
      • 1999 - 2001
      • current position: Assistant Professor, Institute for Microbiology, Innsbruck
    • Anja Forche
      • 1998 - 2000
      • current: postdoctoral associate, Dept. of Biology, Univ. Minnesota
    • James Johnson
      • 1997 - 2000
      • current: Assoc. Professor, Central Washington University, Ellensburg, WA
    • Jianping Xu
      • 1996 - 2000
      • current position: Assistant Professor, McMaster, Univ., Hamilton, Ontario
    • Jean-Marc Moncalvo
      • 1995 - 2002
      • current: Associate Curator, Royal Ontario Museum, Toronto
    • Wendy Untereiner
      • 1995 - 1996
      • current position: assoc. professor, Dept. of Biology, Univ. Manitoba
    • Joseph Spatafora
      • 1992 - 1994
      • current position: Professor, Dept. of Plant Biology, Oregon State Univ
    • Marc Cubeta
      • 1992 - 1994
      • current position: assoc. prof., Dept. of Plant Pathology, NC State University
    • Louise Lewis
      • 1989 - 1992
      • current position: assoc. prof., Dept. of Biology, Univ. of Connecticut
    • Wieland Meyer
      • 1989 - 1992
      • current position: Senior Research Scientist, Univ. Sydney, Australia
    • Steven L. Rehner
      • 1988 - 1989
      • current position: Research Scientist., USDA, Beltsville, MD
    • Marianela Rodriguez
      • 20102012 - present
  • PhD Students

    • Nicholas Pun
      • September, 2013 - present
    • Jessie Uehling
    • Gwendolyn Williams
      • 2007-present
      • Fungal succession during transition from old field to forest
    • Jeri L. Parrent
      • 2006
      • Status: Graduated
      • Ph.D. in 2006: Effects of CO2 enrichment on fungal communities
      • Thesis: Effects of CO2 enrichment on fungal communities
    • Daniel Henk
      • 2000-2005
      • Ph.D recieved 2005, coevolution of fungi and insects
    • Greg Bonito
      • 2003-2008
      • Systematics of Truffles (Tuber). Greg is currently the senior postdoc for our DOE project on Populus mycorrhizae.
    • Jason A Jackson
      • 2005-2010
      • molecular ecology of soil fungi. Jason is now a Research Scientist for the Forest Service.
    • Hannah Reynolds
      • 2005-current
      • Biogeogrpahy and systematics of false truffles in the genus Elaphomyces. Hannah recently graduated and has moved to her new postdoc position where she will be studying the fungal agent of white nose syndrome in bats!
Rytas J. Vilgalys
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